# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:55:01 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 3-{2-[(S)-(4-cyanophenyl)(hydroxy)(1-methyl-1H-imidazol-5-yl)methyl]-5-nitro-1-benzofuran-7-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cncc1[C@](O)(c2oc3c(c2)cc(cc3c4cccc(c4)C#N)[N+]([O-])=O)c5ccc(cc5)C#N
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 NH8  NH8  3-{2-[(S)-(4-cyanophenyl)(hydroxy)(1-methyl-1H-imidazol-5-yl)methyl]-5-nitro-1-benzofuran-7-yl}benzonitrile  ligand  53  36  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NH8
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 NH8  C2   C  CR15   0   0.088  -1.3795   3.1575   2.5746
 NH8  C7   C  CT     0   0.018  -2.3119  -0.1203   1.3251
 NH8  C10  C  CR5    0   0.389  -0.9881  -0.8121   1.0883
 NH8  C11  C  CR15   0  -0.391  -0.5210  -2.0077   1.4986
 NH8  C12  C  CR56   0   0.095   0.8173  -2.1014   0.9897
 NH8  C13  C  CR16   0  -0.376   1.8320  -3.0439   1.0822
 NH8  C14  C  CR6    0   0.277   3.0293  -2.7271   0.4644
 NH8  C15  C  CR16   0  -0.366   3.2429  -1.5292  -0.2241
 NH8  C16  C  CR6    0   0.022   2.2381  -0.5797  -0.3265
 NH8  C21  C  CR6    0   0.056  -3.2207  -0.2421   0.0956
 NH8  C22  C  CR16   0  -0.264  -2.7262  -0.0854  -1.1974
 NH8  C24  C  CR6    0  -0.001  -4.9218  -0.4313  -2.1010
 NH8  C27  C  CSP    0   0.059  -5.7929  -0.5339  -3.2271
 NH8  C31  C  CR6    0   0.105   2.4473   0.7023  -1.0237
 NH8  C32  C  CR16   0  -0.278   1.5130   1.1920  -1.9368
 NH8  C33  C  CR16   0  -0.228   1.7239   2.3952  -2.5926
 NH8  C34  C  CR16   0  -0.244   2.8701   3.1328  -2.3504
 NH8  C35  C  CR6    0   0.028   3.8082   2.6449  -1.4425
 NH8  N1   N  NR5    0  -0.449  -1.3223   1.8128   2.6406
 NH8  N3   N  N      0  -0.446  -2.1252   3.5788   1.5856
 NH8  C4   C  CR15   0  -0.232  -2.5792   2.4495   0.9773
 NH8  C5   C  CR5    0   0.354  -2.0978   1.3367   1.6113
 NH8  C6   C  CH3    0  -0.529  -0.5832   1.0668   3.6382
 NH8  O8   O  OH1    0  -0.639  -2.9119  -0.6861   2.4598
 NH8  O9   O  O      0  -0.453  -0.0532  -0.1331   0.3645
 NH8  C17  C  CR56   0   0.336   1.0401  -0.9097   0.2975
 NH8  C23  C  CR16   0  -0.226  -3.5648  -0.1785  -2.2923
 NH8  C25  C  CR16   0  -0.225  -5.4298  -0.5804  -0.8139
 NH8  C26  C  CR16   0  -0.283  -4.5792  -0.4820   0.2745
 NH8  N28  N  NS     0  -0.247  -6.4971  -0.6175  -4.1350
 NH8  C36  C  CR16   0  -0.295   3.6011   1.4380  -0.7793
 NH8  C37  C  CSP    0   0.055   4.9948   3.3946  -1.1791
 NH8  N38  N  NS     0  -0.246   5.9513   4.0010  -0.9688
 NH8  N41  N  N      1   0.330   4.1203  -3.6873   0.5327
 NH8  O42  O  O     -1  -0.376   3.9379  -4.7105   1.1494
 NH8  O43  O  O      0  -0.376   5.1552  -3.4162  -0.0292
 NH8  H2   H  HCR5   0   0.284  -0.8557   3.7815   3.2838
 NH8  H11  H  HCR5   0   0.286  -1.0328  -2.7401   2.1008
 NH8  H13  H  HCR6   0   0.303   1.6861  -3.9727   1.6141
 NH8  H15  H  HCR6   0   0.301   4.1965  -1.3371  -0.6952
 NH8  H22  H  HCR6   0   0.277  -1.6819   0.1256  -1.3729
 NH8  H32  H  HCR6   0   0.275   0.6227   0.6209  -2.1642
 NH8  H33  H  HCR6   0   0.281   0.9913   2.7572  -3.3004
 NH8  H34  H  HCR6   0   0.288   3.0382   4.0731  -2.8570
 NH8  H4   H  HCR5   0   0.259  -3.2250   2.4892   0.1138
 NH8  H6   H  HCH3   0   0.268  -1.2478   0.4467   4.2327
 NH8  H6A  H  HCH3   0   0.258   0.1741   0.4348   3.1789
 NH8  H6B  H  HCH3   0   0.272  -0.0817   1.7733   4.2936
 NH8  HO8  H  HOH1   0   0.468  -3.1202  -1.6148   2.2961
 NH8  H23  H  HCR6   0   0.286  -3.1679  -0.0536  -3.2902
 NH8  H25  H  HCR6   0   0.286  -6.4834  -0.7683  -0.6610
 NH8  H26  H  HCR6   0   0.278  -4.9958  -0.5892   1.2658
 NH8  H36  H  HCR6   0   0.289   4.3332   1.0842  -0.0651

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 NH8  C2   N1   aromatic  1.348  0.020  1.348
 NH8  C2   N3   aromatic  1.308  0.020  1.308
 NH8  C7   C10  single    1.512  0.020  1.512
 NH8  C7   C21  single    1.534  0.020  1.534
 NH8  C7   C5   single    1.500  0.020  1.500
 NH8  C7   O8   single    1.403  0.020  1.403
 NH8  C10  C11  aromatic  1.348  0.020  1.348
 NH8  C10  O9   aromatic  1.363  0.020  1.363
 NH8  C11  C12  aromatic  1.435  0.020  1.435
 NH8  C12  C13  aromatic  1.388  0.020  1.388
 NH8  C12  C17  aromatic  1.396  0.020  1.396
 NH8  C13  C14  aromatic  1.384  0.020  1.384
 NH8  C14  C15  aromatic  1.398  0.020  1.398
 NH8  C14  N41  single    1.455  0.020  1.455
 NH8  C15  C16  aromatic  1.386  0.020  1.386
 NH8  C16  C31  single    1.474  0.020  1.474
 NH8  C16  C17  aromatic  1.391  0.020  1.391
 NH8  C21  C22  aromatic  1.393  0.020  1.393
 NH8  C21  C26  aromatic  1.391  0.020  1.391
 NH8  C22  C23  aromatic  1.382  0.020  1.382
 NH8  C24  C27  single    1.427  0.020  1.427
 NH8  C24  C23  aromatic  1.394  0.020  1.394
 NH8  C24  C25  aromatic  1.392  0.020  1.392
 NH8  C27  N28  triple    1.152  0.020  1.152
 NH8  C31  C32  aromatic  1.395  0.020  1.395
 NH8  C31  C36  aromatic  1.390  0.020  1.390
 NH8  C32  C33  aromatic  1.387  0.020  1.387
 NH8  C33  C34  aromatic  1.384  0.020  1.384
 NH8  C34  C35  aromatic  1.394  0.020  1.394
 NH8  C35  C36  aromatic  1.393  0.020  1.393
 NH8  C35  C37  single    1.428  0.020  1.428
 NH8  N1   C5   aromatic  1.374  0.020  1.374
 NH8  N1   C6   single    1.448  0.020  1.448
 NH8  N3   C4   aromatic  1.361  0.020  1.361
 NH8  C4   C5   aromatic  1.368  0.020  1.368
 NH8  O9   C17  aromatic  1.343  0.020  1.343
 NH8  C25  C26  aromatic  1.385  0.020  1.385
 NH8  C37  N38  triple    1.152  0.020  1.152
 NH8  N41  O42  single    1.208  0.020  1.208
 NH8  N41  O43  double    1.208  0.020  1.208
 NH8  C2   H2   single    0.930  0.020  1.080
 NH8  C11  H11  single    0.930  0.020  1.080
 NH8  C13  H13  single    0.930  0.020  1.080
 NH8  C15  H15  single    0.930  0.020  1.080
 NH8  C22  H22  single    0.930  0.020  1.080
 NH8  C32  H32  single    0.930  0.020  1.080
 NH8  C33  H33  single    0.930  0.020  1.080
 NH8  C34  H34  single    0.930  0.020  1.080
 NH8  C4   H4   single    0.930  0.020  1.080
 NH8  C6   H6   single    0.970  0.020  1.090
 NH8  C6   H6A  single    0.970  0.020  1.090
 NH8  C6   H6B  single    0.970  0.020  1.090
 NH8  O8   HO8  single    0.850  0.020  0.980
 NH8  C23  H23  single    0.930  0.020  1.080
 NH8  C25  H25  single    0.930  0.020  1.080
 NH8  C26  H26  single    0.930  0.020  1.080
 NH8  C36  H36  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 NH8  H2   C2   N3   125.92  3.000
 NH8  H2   C2   N1   121.58  3.000
 NH8  N3   C2   N1   112.49  3.000
 NH8  O8   C7   C5   107.36  3.000
 NH8  O8   C7   C21  111.28  3.000
 NH8  C5   C7   C21  108.34  3.000
 NH8  O8   C7   C10  108.45  3.000
 NH8  C5   C7   C10  110.44  3.000
 NH8  C21  C7   C10  110.91  3.000
 NH8  O9   C10  C11  111.46  3.000
 NH8  O9   C10  C7   117.09  3.000
 NH8  C11  C10  C7   131.42  3.000
 NH8  H11  C11  C12  126.64  3.000
 NH8  H11  C11  C10  127.49  3.000
 NH8  C12  C11  C10  105.86  3.000
 NH8  C17  C12  C13  119.74  3.000
 NH8  C17  C12  C11  105.60  3.000
 NH8  C13  C12  C11  134.64  3.000
 NH8  H13  C13  C14  122.24  3.000
 NH8  H13  C13  C12  121.19  3.000
 NH8  C14  C13  C12  116.57  3.000
 NH8  N41  C14  C15  118.29  3.000
 NH8  N41  C14  C13  118.46  3.000
 NH8  C15  C14  C13  123.24  3.000
 NH8  H15  C15  C16  119.05  3.000
 NH8  H15  C15  C14  120.12  3.000
 NH8  C16  C15  C14  120.83  3.000
 NH8  C17  C16  C31  122.74  3.000
 NH8  C17  C16  C15  115.39  3.000
 NH8  C31  C16  C15  121.85  3.000
 NH8  C26  C21  C22  119.03  3.000
 NH8  C26  C21  C7   119.29  3.000
 NH8  C22  C21  C7   121.65  3.000
 NH8  H22  C22  C23  118.11  3.000
 NH8  H22  C22  C21  121.07  3.000
 NH8  C23  C22  C21  120.81  3.000
 NH8  C25  C24  C23  120.12  3.000
 NH8  C25  C24  C27  119.95  3.000
 NH8  C23  C24  C27  119.94  3.000
 NH8  N28  C27  C24  180.00  3.000
 NH8  C36  C31  C32  119.03  3.000
 NH8  C36  C31  C16  119.66  3.000
 NH8  C32  C31  C16  121.31  3.000
 NH8  H32  C32  C33  118.94  3.000
 NH8  H32  C32  C31  120.23  3.000
 NH8  C33  C32  C31  120.81  3.000
 NH8  H33  C33  C34  119.81  3.000
 NH8  H33  C33  C32  119.82  3.000
 NH8  C34  C33  C32  120.37  3.000
 NH8  H34  C34  C35  120.33  3.000
 NH8  H34  C34  C33  120.67  3.000
 NH8  C35  C34  C33  119.00  3.000
 NH8  C37  C35  C36  119.39  3.000
 NH8  C37  C35  C34  119.71  3.000
 NH8  C36  C35  C34  120.90  3.000
 NH8  C6   N1   C5   128.72  3.000
 NH8  C6   N1   C2   124.71  3.000
 NH8  C5   N1   C2   106.57  3.000
 NH8  C4   N3   C2   105.12  3.000
 NH8  H4   C4   C5   127.69  3.000
 NH8  H4   C4   N3   121.80  3.000
 NH8  C5   C4   N3   110.51  3.000
 NH8  C4   C5   N1   105.30  3.000
 NH8  C4   C5   C7   130.64  3.000
 NH8  N1   C5   C7   124.06  3.000
 NH8  H6B  C6   H6A  108.13  3.000
 NH8  H6B  C6   H6   108.88  3.000
 NH8  H6A  C6   H6   108.99  3.000
 NH8  H6B  C6   N1   108.43  3.000
 NH8  H6A  C6   N1   111.32  3.000
 NH8  H6   C6   N1   111.02  3.000
 NH8  HO8  O8   C7   110.07  3.000
 NH8  C17  O9   C10  107.26  3.000
 NH8  O9   C17  C16  125.92  3.000
 NH8  O9   C17  C12  109.82  3.000
 NH8  C16  C17  C12  124.23  3.000
 NH8  H23  C23  C24  120.34  3.000
 NH8  H23  C23  C22  120.04  3.000
 NH8  C24  C23  C22  119.62  3.000
 NH8  H25  C25  C26  119.98  3.000
 NH8  H25  C25  C24  120.34  3.000
 NH8  C26  C25  C24  119.68  3.000
 NH8  H26  C26  C25  118.50  3.000
 NH8  H26  C26  C21  120.77  3.000
 NH8  C25  C26  C21  120.73  3.000
 NH8  H36  C36  C35  119.80  3.000
 NH8  H36  C36  C31  120.30  3.000
 NH8  C35  C36  C31  119.89  3.000
 NH8  N38  C37  C35  180.00  3.000
 NH8  O43  N41  O42  123.81  3.000
 NH8  O43  N41  C14  118.18  3.000
 NH8  O42  N41  C14  118.01  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 NH8  CONST_01  C4   C5   N1   C2     0.00   0.0  0
 NH8  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 NH8  CONST_03  C13  C12  C11  C10  180.00   0.0  0
 NH8  CONST_04  C17  C12  C11  C10    0.00   0.0  0
 NH8  CONST_05  C12  C17  O9   C10    0.00   0.0  0
 NH8  CONST_06  C16  C17  O9   C10  180.00   0.0  0
 NH8  CONST_07  C17  O9   C10  C11    0.00   0.0  0
 NH8  CONST_08  C14  C13  C12  C11  180.00   0.0  0
 NH8  CONST_09  C16  C17  C12  C11  180.00   0.0  0
 NH8  CONST_10  O9   C17  C12  C11    0.00   0.0  0
 NH8  CONST_11  O9   C10  C11  C12    0.00   0.0  0
 NH8  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 NH8  CONST_13  C15  C16  C17  C12    0.00   0.0  0
 NH8  CONST_14  C31  C16  C17  C12  180.00   0.0  0
 NH8  CONST_15  C16  C17  C12  C13    0.00   0.0  0
 NH8  CONST_16  O9   C17  C12  C13  180.00   0.0  0
 NH8  CONST_17  C16  C15  C14  C13    0.00   0.0  0
 NH8  CONST_18  C17  C12  C13  C14    0.00   0.0  0
 NH8  CONST_19  C31  C16  C15  C14  180.00   0.0  0
 NH8  CONST_20  C17  C16  C15  C14    0.00   0.0  0
 NH8  CONST_23  O9   C17  C16  C15  180.00   0.0  0
 NH8  CONST_24  C33  C32  C31  C16  180.00   0.0  0
 NH8  CONST_25  C35  C36  C31  C16  180.00   0.0  0
 NH8  CONST_26  C24  C23  C22  C21    0.00   0.0  0
 NH8  CONST_27  C24  C25  C26  C21    0.00   0.0  0
 NH8  CONST_28  C25  C26  C21  C22    0.00   0.0  0
 NH8  CONST_29  C25  C24  C23  C22    0.00   0.0  0
 NH8  CONST_30  O9   C17  C16  C31    0.00   0.0  0
 NH8  CONST_31  C34  C33  C32  C31    0.00   0.0  0
 NH8  CONST_32  C34  C35  C36  C31    0.00   0.0  0
 NH8  CONST_34  C35  C36  C31  C32    0.00   0.0  0
 NH8  CONST_35  C35  C34  C33  C32    0.00   0.0  0
 NH8  CONST_36  C36  C31  C32  C33    0.00   0.0  0
 NH8  CONST_37  C36  C35  C34  C33    0.00   0.0  0
 NH8  CONST_38  C4   N3   C2   N1     0.00   0.0  0
 NH8  CONST_39  N3   C4   C5   N1     0.00   0.0  0
 NH8  CONST_40  C5   N1   C2   N3     0.00   0.0  0
 NH8  CONST_42  C26  C21  C22  C23    0.00   0.0  0
 NH8  CONST_43  C26  C25  C24  C23    0.00   0.0  0
 NH8  CONST_44  C7   C5   N1   C2   180.00   0.0  0
 NH8  CONST_45  C12  C11  C10  C7   180.00   0.0  0
 NH8  CONST_46  C17  O9   C10  C7   180.00   0.0  0
 NH8  CONST_47  C23  C22  C21  C7   180.00   0.0  0
 NH8  CONST_48  C25  C26  C21  C7   180.00   0.0  0
 NH8  CONST_49  N3   C4   C5   C7   180.00   0.0  0
 NH8  CONST_50  N41  C14  C13  C12  180.00   0.0  0
 NH8  CONST_51  N41  C14  C15  C16  180.00   0.0  0
 NH8  CONST_52  C27  C24  C23  C22  180.00   0.0  0
 NH8  CONST_53  C26  C25  C24  C27  180.00   0.0  0
 NH8  CONST_54  C37  C35  C36  C31  180.00   0.0  0
 NH8  CONST_55  C37  C35  C34  C33  180.00   0.0  0
 NH8  CONST_56  C6   N1   C2   N3   180.00   0.0  0
 NH8  CONST_57  C6   N1   C5   C4   180.00   0.0  0
 NH8  CONST_58  H4   C4   N3   C2   180.00   0.0  0
 NH8  CONST_59  H13  C13  C12  C11    0.00   0.0  0
 NH8  CONST_60  H11  C11  C12  C13    0.00   0.0  0
 NH8  CONST_61  H15  C15  C14  C13  180.00   0.0  0
 NH8  CONST_62  H32  C32  C31  C16    0.00   0.0  0
 NH8  CONST_63  H36  C36  C31  C16    0.00   0.0  0
 NH8  CONST_64  H23  C23  C22  C21  180.00   0.0  0
 NH8  CONST_65  H25  C25  C26  C21  180.00   0.0  0
 NH8  CONST_66  H26  C26  C21  C22  180.00   0.0  0
 NH8  CONST_67  H22  C22  C23  C24  180.00   0.0  0
 NH8  CONST_68  H33  C33  C32  C31  180.00   0.0  0
 NH8  CONST_69  H34  C34  C33  C32  180.00   0.0  0
 NH8  CONST_70  H2   C2   N3   C4   180.00   0.0  0
 NH8  CONST_71  O42  N41  C14  C13    0.00   0.0  0
 NH8  CONST_72  O43  N41  C14  C13  180.00   0.0  0
 NH8  CONST_73  O42  N41  C14  C15  180.00   0.0  0
 NH8  CONST_74  O43  N41  C14  C15    0.00   0.0  0
 NH8  Var_01    H6   C6   N1   C2   118.51  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NH8  chir_01  C7  C21  C5  C10  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 NH8  plan-1  C2   0.020
 NH8  plan-1  C7   0.020
 NH8  plan-1  N1   0.020
 NH8  plan-1  N3   0.020
 NH8  plan-1  C4   0.020
 NH8  plan-1  C5   0.020
 NH8  plan-1  C6   0.020
 NH8  plan-1  H2   0.020
 NH8  plan-1  H4   0.020
 NH8  plan-2  C7   0.020
 NH8  plan-2  C21  0.020
 NH8  plan-2  C22  0.020
 NH8  plan-2  C24  0.020
 NH8  plan-2  C27  0.020
 NH8  plan-2  C23  0.020
 NH8  plan-2  C25  0.020
 NH8  plan-2  C26  0.020
 NH8  plan-2  N28  0.020
 NH8  plan-2  H22  0.020
 NH8  plan-2  H23  0.020
 NH8  plan-2  H25  0.020
 NH8  plan-2  H26  0.020
 NH8  plan-3  C16  0.020
 NH8  plan-3  C31  0.020
 NH8  plan-3  C32  0.020
 NH8  plan-3  C33  0.020
 NH8  plan-3  C34  0.020
 NH8  plan-3  C35  0.020
 NH8  plan-3  C36  0.020
 NH8  plan-3  C37  0.020
 NH8  plan-3  N38  0.020
 NH8  plan-3  H32  0.020
 NH8  plan-3  H33  0.020
 NH8  plan-3  H34  0.020
 NH8  plan-3  H36  0.020
 NH8  plan-4  C7   0.020
 NH8  plan-4  C10  0.020
 NH8  plan-4  C11  0.020
 NH8  plan-4  C12  0.020
 NH8  plan-4  C13  0.020
 NH8  plan-4  C14  0.020
 NH8  plan-4  C15  0.020
 NH8  plan-4  C16  0.020
 NH8  plan-4  C31  0.020
 NH8  plan-4  O9   0.020
 NH8  plan-4  C17  0.020
 NH8  plan-4  N41  0.020
 NH8  plan-4  H11  0.020
 NH8  plan-4  H13  0.020
 NH8  plan-4  H15  0.020
 NH8  plan-5  C14  0.020
 NH8  plan-5  N41  0.020
 NH8  plan-5  O42  0.020
 NH8  plan-5  O43  0.020

